.pull-left[ ] .pull-right[
]
Regions may be added to “Regions of interest”
These act as bookmarks for areas of particular interest
.pull-left[ ] .pull-right[
]
.pull-left[ ] .pull-right[
]
.pull-left[ - IGV allows the inclusion of information on samples. - Sample information is included in sample information panel.] .pull-right[ ] — ## Loading Sample Metadata
Example Sample information file http://www.broadinstitute.org/igvdata/exampleFiles/exampleSampleInfo.txt
Sample information can include discrete and continuous.
Can be used to “sort” and “filter” tracks.
Can split tracks across panels by “group”
** Load data from a URL ** - As with UCSC, IGV supports data hosted on external servers. - Data accessible from a URL such as HTTP and FTP can be loaded using the “Load from URL”.
** Load data from a server (IGV/Encode servers).**
Unlike UCSC, IGV comes with few external tracks.
External tracks (relevant to the genome) can be loaded from the IGV server or Encode-IGV server.
IGV associates common file formats with default display methods.
Most of the time IGV will make a sensible choice how we wish to display data.
.pull-left[ - Basic - Tab-delimited - Chrom,Start,End - Bed6 - bigBed (recommended)] .pull-right[
.pull-left[ - Wig/bedGraph require high memory load - Recommended format is bigWig] .pull-right[
.pull-left[ - BAM files contain alignment information. - Require an accompanying .bai index file for display] .pull-right[
]
** General **
** Alignments **
** Graph/interval files** - Graph type
IGV can be used to combine tracks